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A federal judge on Thursday tossed a scathing $680 million lawsuit filed by 34 ex-students of Yeshiva University’s prestigious all-boys high school who allege honchos there covered up decades of sexual and physical abuse.

Manhattan federal Judge John Koeltl in his 52-page legal opinion said the victims — who range in age from late-30s to early-60s and reside as far as Israel – simply waited too long to speak up.

“Statutes of limitations strike a balance between providing a reasonable time for victims to bring their claims while assuring that defendants have a fair opportunity to defend themselves before evidence is lost or memories fade,” Koeltl said “In this case, the statutes of limitations have expired decades ago, and no exceptions apply.”

After the written decision, Kevin Mulhearn, the plaintiffs’ lawyer, called Koeltl’s decision an “abomination and a disgrace” and said he plans to appeal.

“The court has stood up and said to Yeshiva University, ‘Congratulations, you have succeeded in your cover-up of the sex abuse!” he said.

“The court has set an impossible standard in dealing with a cover-up situation. I think this decision is intellectually dishonest, wrongheaded and potentially dangerous by giving schools incentives to cover up the sexual abuse of their employees.”

The suit, which was filed in July, alleges the university willfully turned a blind eye while two of its rabbis sexually assaulted then-teenage boys at the Marsha Stern Talmudical Academy in Manhattan between 1969 and 1989.

Some of the plaintiffs allege they were attacked by Rabbi Macy Gordon, a former teacher who is accused of sodomizing one victim with a toothbrush during a violent attack in a school dorm room. The suit alleges that the victim and his father reported the attack to the school in 1980 — but that officials failed to report it to authorities and that Gordon sexually brutalized at least one other boy.

Other plaintiffs claim they were attacked by Rabbi George Finkelstein, a former principal at the high school, or Richard Andron, a former university student and friend of Finkelstein who was allegedly allowed to roam freely in the school’s hallways and dorms.

The students say they only decided to come forward decades after the alleged incidents after learning they were not alone following a December 2012 story in the Jewish newspaper The Forward in which then-Yeshiva University Chancellor Norman Lamm acknowledged both rabbis were allowed to leave quietly after students accused them of sex abuse. Lamm retired on July 1.

Koeltl did not immediately return messages, but one of his staffers said he makes it a practice of not commenting on his decisions.

Yeshiva officials in a statement said they are “gratified” by the ruling, adding “our thoughts and remorse remain with those affected and harmed, and the confidential counseling services of Yeshiva University remain available to them.”